                      :-) GROMACS - gmx mdrun, 2021.5 (-:

                            GROMACS is written by:
     Andrey Alekseenko              Emile Apol              Rossen Apostolov     
         Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
       Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
     Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
    Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
       Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
      Aleksei Iupinov           Christoph Junghans             Joe Jordan        
    Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
      Carsten Kutzner              Per Larsson              Justin A. Lemkul     
       Viveca Lindahl            Magnus Lundborg             Erik Marklund       
        Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
        Szilard Pall               Sander Pronk              Roland Schulz       
       Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
       Peter Tieleman              Jon Vincent              Teemu Virolainen     
     Christian Wennberg            Maarten Wolf              Artem Zhmurov       
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2021.5
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /media/romi/My Book Duo/completed-simulation-oracle/14-7-23/5tl5/312k
Process ID:   44820
Command line:
  gmx mdrun -deffnm md_1_20 -cpi md_0_10.cpt -noappend -v

GROMACS version:    2021.5
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        CUDA
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 9.4.0
C compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 9.4.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -fopenmp -O3 -DNDEBUG
CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2020 NVIDIA Corporation;Built on Mon_Nov_30_19:08:53_PST_2020;Cuda compilation tools, release 11.2, V11.2.67;Build cuda_11.2.r11.2/compiler.29373293_0
CUDA compiler flags:-std=c++17;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=sm_75;-gencode;arch=compute_80,code=sm_80;-Wno-deprecated-gpu-targets;-gencode;arch=compute_86,code=sm_86;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_53,code=compute_53;-gencode;arch=compute_80,code=compute_80;-use_fast_math;-D_FORCE_INLINES;-mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -pthread -fopenmp -O3 -DNDEBUG
CUDA driver:        11.40
CUDA runtime:       11.20


Running on 1 node with total 20 cores, 20 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  12th Gen Intel(R) Core(TM) i7-12700K
    Family: 6   Model: 151   Stepping: 2
    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Only logical processor count
  GPU info:
    Number of GPUs detected: 1
    #0: NVIDIA NVIDIA GeForce RTX 3070 Ti, compute cap.: 8.6, ECC:  no, stat: compatible


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.5850051
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 50050000
   init-step                      = 0
   simulation-part                = 1
   mts                            = false
   comm-mode                      = Linear
   nstcomm                        = 100
   bd-fric                        = 0
   ld-seed                        = 1636582041
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 0
   nstvout                        = 0
   nstfout                        = 0
   nstlog                         = 5000
   nstcalcenergy                  = 100
   nstenergy                      = 5000
   nstxout-compressed             = 5000
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 10
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Potential-shift
   rvdw-switch                    = 0
   rvdw                           = 1
   DispCorr                       = EnerPres
   table-extension                = 1
   fourierspacing                 = 0.16
   fourier-nx                     = 96
   fourier-ny                     = 96
   fourier-nz                     = 96
   pme-order                      = 4
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 0
   epsilon-surface                = 0
   tcoupl                         = V-rescale
   nsttcouple                     = 10
   nh-chain-length                = 0
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 2
   compressibility (3x3):
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = No
   posres-com (3):
      posres-com[0]= 0.00000e+00
      posres-com[1]= 0.00000e+00
      posres-com[2]= 0.00000e+00
   posres-comB (3):
      posres-comB[0]= 0.00000e+00
      posres-comB[1]= 0.00000e+00
      posres-comB[2]= 0.00000e+00
   QMMM                           = false
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = true
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   awh                            = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
   applied-forces:
     electric-field:
       x:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       y:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       z:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
grpopts:
   nrdf:     20184.9      448029
   ref-t:         312         312
   tau-t:         0.1         0.1
annealing:          No          No
annealing-npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0


Reading checkpoint file md_0_10.cpt
  file generated by:     /usr/bin/gmx
  file generated at:     Sun Jun 18 07:49:16 2023

  GROMACS double prec.:  0
  simulation part #:     1
  step:                  50000000
  time:                  100000.000000

  Version mismatch,
    current program: 2021.5
    checkpoint file: 2019.6

The current GROMACS major version is not identical to the one that
generated the checkpoint file. In principle GROMACS does not support
continuation from checkpoints between different versions, so we advise
against this. If you still want to try your luck we recommend that you use
the -noappend flag to keep your output files from the two versions separate.
This might also work around errors where the output fields in the energy
file have changed between the different versions.

Changing nstlist from 10 to 100, rlist from 1 to 1.166

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
  PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 20 OpenMP threads 

Pinning threads with an auto-selected logical core stride of 1
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073

Generated table with 1083 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1083 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1083 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Long Range LJ corr.: <C6> 3.0676e-04


Using GPU 8x8 nonbonded short-range kernels

Using a dual 8x8 pair-list setup updated with dynamic, rolling pruning:
  outer list: updated every 100 steps, buffer 0.166 nm, rlist 1.166 nm
  inner list: updated every  10 steps, buffer 0.001 nm, rlist 1.001 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  outer list: updated every 100 steps, buffer 0.320 nm, rlist 1.320 nm
  inner list: updated every  10 steps, buffer 0.043 nm, rlist 1.043 nm

Using Lorentz-Berthelot Lennard-Jones combination rule

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 3929

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 232053 Atoms
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

Started mdrun on rank 0 Mon Sep 18 10:35:29 2023

           Step           Time
       50000000   100000.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    6.86031e+03    1.84429e+04    1.24288e+04    1.22744e+03   -3.15697e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    5.57228e+03    1.16386e+05    5.17124e+05   -2.90517e+04   -3.76629e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.08255e+04   -3.09963e+06    6.06470e+05   -2.49316e+06    4.78910e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11574e+02   -2.03046e+02    3.91242e+01    3.91040e-06

step 50002300: timed with pme grid 96 96 96, coulomb cutoff 1.000: 793.8 M-cycles
step 50002500: timed with pme grid 80 80 80, coulomb cutoff 1.171: 926.8 M-cycles
step 50002700: timed with pme grid 84 84 84, coulomb cutoff 1.115: 895.4 M-cycles


Received the INT signal, stopping within 100 steps

           Step           Time
       50002800   100005.60000

Writing checkpoint, step 50002800 at Mon Sep 18 10:35:37 2023


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    6.49667e+03    1.83739e+04    1.25863e+04    1.15834e+03   -3.19623e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    5.51369e+03    1.16431e+05    5.11229e+05   -2.90057e+04   -3.75504e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.09813e+04   -3.09448e+06    6.06478e+05   -2.48800e+06    4.78909e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11578e+02   -2.02405e+02   -8.99697e+01    4.07429e-06


Energy conservation over simulation part #2 of length 5.6 ns, time 100000 to 100006 ns
  Conserved energy drift: -8.08e-06 kJ/mol/ps per atom


	<======  ###############  ==>
	<====  A V E R A G E S  ====>
	<==  ###############  ======>

	Statistics over 2801 steps using 29 frames

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    6.69125e+03    1.85666e+04    1.25022e+04    1.14492e+03   -3.15487e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    5.61225e+03    1.16265e+05    5.15707e+05   -2.90399e+04   -3.76160e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    1.98577e+04   -3.09745e+06    6.07065e+05   -2.49038e+06    4.78911e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11879e+02   -2.02881e+02    3.72520e+00    0.00000e+00

          Box-X          Box-Y          Box-Z
    1.49859e+01    1.49859e+01    1.05966e+01

   Total Virial (kJ/mol)
    2.02114e+05    5.26235e+01    4.35321e+02
    5.55513e+01    2.02700e+05   -3.83370e+02
    4.38412e+02   -3.82779e+02    2.01456e+05

   Pressure (bar)
    5.35178e+00   -3.03002e+00   -6.88251e+00
   -3.07088e+00   -4.95268e+00    6.79125e+00
   -6.92565e+00    6.78299e+00    1.07765e+01

      T-Protein  T-non-Protein
    3.12488e+02    3.11852e+02


	M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V&F=Potential and force  V=Potential only  F=Force only

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Pair Search distance check             635.783536        5722.052     0.0
 NxN Ewald Elec. + LJ [F]            639637.042176    42216044.784    98.0
 NxN Ewald Elec. + LJ [V&F]            6684.208448      715210.304     1.7
 1,4 nonbonded interactions              59.529653        5357.669     0.0
 Shift-X                                  6.729537          40.377     0.0
 Bonds                                   11.820220         697.393     0.0
 Propers                                 50.698100       11609.865     0.0
 Impropers                                3.826166         795.843     0.0
 Virial                                  65.219538        1173.952     0.0
 Stop-CM                                  6.729537          67.295     0.0
 Calc-Ekin                              130.413786        3521.172     0.0
 Lincs                                   11.005129         660.308     0.0
 Lincs-Mat                               54.653112         218.612     0.0
 Constraint-V                           649.470671        5845.236     0.0
 Constraint-Vir                          64.051702        1537.241     0.0
 Settle                                 209.153471       77386.784     0.2
 CMAP                                     1.504137        2557.033     0.0
 Urey-Bradley                            41.166297        7533.432     0.0
-----------------------------------------------------------------------------
 Total                                                43055979.352   100.0
-----------------------------------------------------------------------------


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 1 MPI rank, each using 20 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Neighbor search        1   20         29       0.214         15.428   2.5
 Launch GPU ops.        1   20       2801       0.174         12.530   2.0
 Force                  1   20       2801       0.407         29.393   4.7
 Wait PME GPU gather    1   20       2801       0.841         60.696   9.7
 Reduce GPU PME F       1   20       2801       0.279         20.168   3.2
 Wait GPU NB local                              0.889         64.166  10.3
 NB X/F buffer ops.     1   20       5573       1.181         85.286  13.7
 Write traj.            1   20          2       0.340         24.568   3.9
 Update                 1   20       2801       0.323         23.301   3.7
 Constraints            1   20       2801       0.371         26.785   4.3
 Rest                                           3.614        260.920  41.9
-----------------------------------------------------------------------------
 Total                                          8.633        623.242 100.0
-----------------------------------------------------------------------------

               Core t (s)   Wall t (s)        (%)
       Time:      172.661        8.633     2000.0
                 (ns/day)    (hour/ns)
Performance:       56.064        0.428
Finished mdrun on rank 0 Mon Sep 18 10:35:38 2023

